Naruto: Phantom Of the Leaf
by Jiraiya's Lost Student
Summary: Danzo Succeeded in putting Naruto into Anbu from birth, But he is under Sarutobi Direction and two mysterious Anbu's care. But why has Danzo folded and given up his weapon? Maybe he didn't, maybe he had it planned all along? Now Naruto is swept up in a game of chess that he has no control over. Graduating from the Academy at the youngest age ever, how will Naruto coup with Itachi?
1. Chapter 1

Standard Bullshit: I own the mother of whatever FCC reads this...

* * *

"Silence!" shouted Hizuren Sarutobi, third and now acting hokage. "I just battled the kyuubi, lost my predecessor, lost the best ANBU commander this village has ever had, along with countless other loved ones, including my wife, and am in no mood to deal with the petty scwabling of you selfish people! Now anything that is related to the village may be discussed now, and if I hear one word of anything I deem even remotely selfish, I will show you all why I am known as The God of shinobi!"

There was a moment of silence as the council members regained there composer. Haishi hyuga was the first to speak. "Lord hokage, do we know the amount of shinobi lost in the attack?"

"Roughly fifteen percent of our jonin, fifteen percent of our chunin and thankfully only two squads of genin that were doing a d rank late into the night." stated Sarutobi, reading a report handed to him one of his most loyal ANBU, Phoenix.

"Sir, from Dragon's preliminary estimates, there are Fourty five civilians dead and several dozen injured." stated Phoenix, his voice relatively deep. "Most of the civilians killed where next to the wall that got knocked over, the injuries range from rolled ankle to one unfortunate young woman who had a railing segment impale her chest. She most likely won't make it through the night."

"Lets hope that number stays low. Thank you Phoenix, can you check and see our losses of ANBU? And make sure that the battlefield is documented." stated Sarutobi, Phoenix simply nodded and disapeared in a flash of lightning.

"With us being so low on millitary power, we should change the academy standards. The more we can graduate, the fast we can rebuild our strength." stated Danzo, attempting to gain more subjects.

"No. I will not have this village become another Iwa. If it comes down to it, I would rather have less shinobi that are more skilled than a platoon of fodder." stated Sarutobi seriously.

"Then I suggest we turn the demon container into a weapon. Minato gave us a Jinchuuruki, we should use it." stated Fugaku Uchiha "I volunteer the Uchiha clan to raise the child."

"Of course you would. After all, the Uchiha lost the least of all the clans, even though your compound was the closest to the attack..." stated Haishi, whose clan had lost many members.

"Are you insinuating that we had something to do with this?" questioned Fugaku dangerously, his sharingan activating.

"Seize this bickering at once! From the reports, the Uchiha were all in different parts of the village, as we're the hyuga." stated Sarutobi, already regaining his headache.

"And who filed the report? An Uchiha?" questioned Haishi, his eyes never leaving Fugaku.

"No, it was dragon. Says right here that only ten or so Uchiha went up against the kyuubi, and all but one died. The rest stayed back, helping civilians get to the bunkers. Seeing as the Uchiha are the police force, it makes sense that the civilians would trust them." stated Inoichi as he looked over the report. "If anyone would want to make the Uchiha look bad, it would be Dragon."

"Never the less. No one clan can raise Naruto. And seeing as you all seem adamant on turning young naruto into a trump card do to our lowered military power... I suggest he be enlisted in ANBU." stated Sarutobi. Mass hysteria started immediately, but was quelled by a voice at the door

"I'd be delighted to look over young naruto. And I'm sure that Kakashi would be too. How about you dragon?" questioned Phoenix, his voice deep as usual, though now it held the sound of playfulness to it.

"Probably not the best idea, seeing as I can barely take care of my self, but I'll guard that little son of a bitch with my life." stated Dragon, immediately being punched into a wall by Phoenix.

"Don't insult my sensei." stated Pheonix.

Dragon pulled himself out of the wall, jumped to his feet and walked back to phoenixes side. "It's a figure of speech. And just because your temporary commander until they find some poor soul to replace Kushina-neechan, does not mean you can just go around punching people."

"I havnt punched any people. Just you, oh lord of the chipmunks." stated Phoenix mockingly while fake bowing.

"For the last fucking time! They are not chipmunks!" shouted Dragon as he began flashing through handsigns.

"Enough!" shouted Sarutobi. Usually he enjoyed the antics of the two odd shinobi, though he already had a headache from the council and this was only making it worse.

Both Phoenix and dragon promptly settled down, straightened up and and stood at attention.

"Hokage sama. As head of the Uchiha clan, I cannot allow those two to raise this boy." stated Fugaku.

"Oh? And why is that?" questioned Phoenix, who was now sitting in the vacant Uzumaki seat. Odd thing was, no one had seen him move... "And I swear on the old mans life that if you say that I'm not strong enough, or even begin to comment on dragons problem, that you're clan caused by the way, I will kill you myself."

"You are threatening a clan head BOY! I suggest you change your tone." stated Fugaku

"And you just threatened the current commander of ANBU. Make no mistake, I earned this position by having a flawless record sense I was a genin, an achievement only four others have ever achieved, one of whom just got behind you without you noticing, and the other two have recently died." stated Phoenix everyone looked behind Fugaku, only to see Dragon silently spinning a demon wind shuruken in his right hand.

"My mind may be scattered do to a member of your clan attempting a stolen Jutsu on me, but when needed, I can be civil, something you're clan knows nothing about." stated Dragon.

"Both of you stand down, if it were any other day you could proceed, but we just lost a huge chunk of our military power, and I need you two free of trouble." stated Sarutobi, before he was done speaking, both ANBU members were already back to their spots at the end of table. "Good. Now dragon, put down that saw blade."

Dragon looked at his right hand, which still held the spinning chunk of metal, back to Sarutobi, then back to his right hand. He stopped its spin, folded it up and attached it to his belt.

"Good. Now Phoenix, as acting commander of ANBU, you will have the reports on my desk tomorrow, I also want a list of every promotion you believe that has been earned tonight. From this point till he becomes a jonin, he will be simply known as Naruto, Dragon, prepare a room for naruto in block C, and for gods sakes, not next to Cheetah!"

* * *

(This is not a priority, this will not be updated Regularly.)


	2. Chapter 2

Boner

* * *

-Three years later-

"Naruto... I have some very bad news." Stated a dog masked Anbu. The boy he was talking to was sitting in a meditative position in the center of his room. He wore standard ANBU gear, only it was tailored to fit his surprisingly muscular and proportionate three year old frame.

"Phoenix and Dragon are missing, arnt they uncle kakashi?" Questioned naruto, his tone depressed. His voice did not belong to that of a three year old. Each word was crisp and clear, yet still childish in sound.

Dog removed his mask, reveling the sharingan eye of kakashi hatake, Narutos legal guardian. "Were not sure. They didn't come back from their last mission." 'He already knew? How? We just learned about it an hour ago...'

"I felt it Uncle Kakashi... Their chakras flared then disappeared... I think that they are in the village. They fell like they are underground..." stated Naruto. "Who we're they on a mission with?"

"We've already looked into that. Neither Iguana or rat made it back either." stated Kakashi. Naruto only nodded. "Naruto... Now that phoenix and dragon are missing... Myself and lord Sandaime have chosen to have you placed in an academy class to become a genin." 'If it will keep him from Danzo, I'll become a genin too.'

"I understand... Does that mean I have to move out?" questioned the three year old. "I don't want to uncle kakashi... I like it here..."

"No, you may continue living here until you reach jonin level when it will be safe to reveal you're identity." stated Kakashi, sitting next to the small boy on the bed.

"Can I still use all my Jutsu?" questioned Naruto, a ray of hope in his eyes.

"All but the Rasengan and if you manage to use the Hiraishin. It's publicly known that you were raised by us five, so the other Jutsu are alright to use." stated Kakashi with an eye smile, ruffling the blades hair. "But use them sparingly. Your resurves just arnt big enough to use them effectively yet."

"Even Raikiri?" questioned Naruto

"As long as you follow the stipulations. But remember, even if you can use the Kyuubis chakra, you should relay on you're own power. I myself am already starting to relay on this eye, so make sure you only use his chakra in training or if it's an emergency."

* * *

-Next day-

"Ok class. Today we have a new student joining us, so try and make him feel welcome." stated the chunin instructor. He opened the door and a tiny ANBU minus the mask walked in.

"Awe, sensei! You never said you had a kid!" called out a girl in the back of the room. "Look! He looks like a little ANBU."

Naruto quickly observed his surroundings. 'only seventeen kids, eighteen with me...' Moving faster than all but one of the academy students could see, Naruto was on a knee on the desk in front of the girl who was previously talking. "Hi, my name is Naruto. I'm you're new classmate, mind if I take the seat next to you?"

The whole class was silent. A child, a literal three year old, just moved faster than they could see. And spoke clearly and confidently. Was this the boy their parents had told them about?

"Alright class. As I said before, we have a new student joining us today. He will be taking the graduation exam with you next -cough- month." stated Gekko Hayate, the chunin instructor. "Naruto, please take the seat next to miss inuzuka so we can began?"

"Sure." states Naruto as he moved from the table to the seat with a spinning flip. "Hows that cold coming along sensei?"

"Dont know, I've had it for a week now." stated Gekko. "You came at a very good time Naruto, we're about to do a mock graduation exam, minus the paper test."

'Interesting, he looks just like a chibi uncle Minato...' thought Itachi as he studied the blonde. 'I will have to ask mother, if anyone would know, it would be her.'

'He's so fast!' thought Hana as she gazed at the toddler next to her. 'It shouldn't be possible... He's not that much older than Kiba, yet he's much more proportionate and as fast as Hayate-Sensei.'

* * *

-One month later-

"Alright , that was much better Hana. Six shuruken and six kunai. Up next is Itachi." Stated Hayate.

'The Uchiha... My god brother as well... I wander if he knew mom?' thought Naruto as he watched Itachi throw the weapons. 'he's good...'

"As always, very good Itachi, ten shuruken and nine kunai. Naruto if you would be so kind. And don't use chakra." stated Gekko with a sweatdrop, remembering the time the tiny blonde had coated his kunai in wind chakra and went right through the target... And the shed behind it... And the trees behind that.

"You're no fun sensei." states naruto as he picked up a set of shuruken and threw all ten at the same time, each one hitting a bullseye. He then picked up the kunai and threw two at a time, each one landing in the hole of a shuruken.

The class stood wide eyed at the display by the three year old. Any who had questions about the kid were instantly shut up by the show he just put on.

"Figures. It's unfair that you're testing for genin." stated Gekko with a smirk. He had been one of the five that helped raise him, and had tried to teach the blonde his sword style, though Naruto didn't take the style up very well and ended up Just learning the basics.

"Hey, blame the old man. He's the one that set this up." stated naruto with a shrug. "Although, if it hadn't been for you all, I don't believe that would be this good until I was at least ten."

Naruto proceeded to watch the students fight. It might seem odd to most, but the three year old was already studying his classmates skills for future use. 'The inuzuka is very skilled, probably the best behind-'

"Naruto Uzumaki versus Itachi Uchiha!" called out Hayate "No Jutsu allowed! Don't -cough- test me."

Naruto and Itachi squared off, the three year old making sure to stay out of the much taller boys reach, Itachi making sure to keep his eyes focused in the blonde, who could seemingly disappear and take you down before you could even blink.

"Begin."

Naruto was behind Itachi in the blink of an eye, sending a kick at the back of the older boys head. Itachi barely ducked the kick and retaliated with an elbow aimed at Narutos head. Naruto caught the elbow in his armpit, trapping the Uchihas arm. He then used his small frame to leverage his lower body up, kicking Itachi in the face and wrapping his legs around the older boys throat.

'Hes so strong! I can't even breath! Gotta do something!' thought Itachi. He tryed to swing at the blonde but naruto had positioned himself so that the only thing he could hit we're his legs, and Itachi need air quickly.

Everyone was shocked watching the match. None of them had seen naruto fight before, only glimpses of his speed. Add to the fact he was only three years old and was utilizing his small frame to choke out none other than the Uchiha protege, and you have one stuned crowd.

The excitement was taken up a notch when Itachi jumped high in the air and forced himself to land on naruto, who once again showed great speed and reflexes by using his grip on Itachis neck to pull himself up, releasing the Uchihas arm and catapulting himself away from the descending Uchiha, both boys landing on their feet.

"You're good. Hayate sensei, I beleive that's enough for me to pass. Itachi wins." stated Naruto as he walked over to the the edge of the ring and stepped out. 'It's better I don't show all of my tricks off the bat. I need an edge if I need to fight any of these people in the future.'

"Winner, Itachi Uchiha." stated Gekko, looking at the tiny blonde. 'Still hiding your strength... Smart kid.'

* * *

-Hokages office-

"What do you think of him?" questioned Hiruzen. He and the other people looking into his crystal ball.

In the office stood Kakashi Hatake, Maito Gai, Mikoto Uchiha, Danzo Shimura and Raimo Sarutobi.

"Dad, you already know what we think of the brat. Why ask?" Questioned Raimo, who was keeping an eye on Danzo.

"Because one of you will be the boys sensei." States Danzo, shocking the group.

"Any idea on who is going to be on his team?" Questioned Mikoto, the thirty year old mother of Itachi and god mother of naruto.

"The only two he works well with are Hana Inuzuka and your son Itachi. Though he has shown reasonable team work with most students. I believe the boys have a bit of a rivalry going, and he seems to view Hana as a big sister, though that's probably because she's the only girl in his life that still treats him like the three year old he is. And although it pains me to say this, Itachi and Hana are the only ones that Naruto considers anything other than classmates." Stated the older sarutobi.

"Indeed, also, because of his late entry into the academy, he will be the statistical dead last." stated Danzo.

"Count me out. My wife is pregnant with our first and I wouldn't have the time." Stated Raimo, who then walked out the door, leaving the two teens and mother with his father and one time sensei.

"I already taught Naruto much. Once his reserves come in he will be high jonin in ninjutsu, after all, he already can do Rasengan and rikiri, even if it is only once a day. Plus I already spend almost all of my time off With him now, after..." Trailed off kakashi, remembering his late friends.

"I believe I am in the same boat as my rival Hokage sama. Other than taijutsu, there is not much Naruto doesn't already know. Plus if he does land on the team you mentioned, both the Inuzuka and Uchiha have their own taijutsu styles." Stated Gai, his voice booming through the building.

"I believe that just leaves me." Stated Mikoto. "I'd love to teach my son and god son, but I need to know what naruto-Chan is capable of. I am well aware of who raised and trained him. I need to be sure that he can take care of himself, especially with how much work Hana will have to do if she is going to catch up to Itachi, let alone naruto."

"Then it's settled. You may test you're team tomorrow after team assignments." Stated Sarutobi.

"This will work out well. The villagers will be more relaxed about Naruto-kun becoming a ninja with Itachi at his side, though young Hana may have a problem when she gets her companions do to the foxes presence." stated Danzo before looking to Kakashi. "Have your summons said anything about it?"

"No, though Pakkun stated that Naruto smells like Toads and... What he assumes is dragons m. I'm not sure what that is about though." stated Kakashi seriously.

"Hmm, Phoenix didn't have a contract, and Dragons contract is most certainly not dragons, Dispite his name..." stated Sarutobi "I will ask Enma if he knows of this. For now we will continue his training. Danzo, you and Mikoto will have to create a schedule so that naruto can balance out his studies as well as continue his growth."

* * *

-Later that night-

"Kaa-San! I'm home." Called out Itachi as he walked in to his home. His father was still at work, but he could hear his little brother run toward him.

"Nii-San! Did you graduate?" Questioned Sasuke.

"Yes I did. Most likely at the top of my class." Stated Itachi with a smile. He truly did love his brother, but it was only a matter of time before he would ask him again for training.

"Is it true what father said? That someone my age is graduating with you?" questioned Sasuke.

"Yes. His name is naruto. Ask mother about him." stated Itachi With a small smile as he moved to his room to change into something that wasn't soaking wet from training.

"Kaa San? Is it true that there's a boy my age that's as strong as Itachi?" Questioned Sasuke loudly, not moving from the spot he was already in.

"I don't know how strong he is dear, but he did graduate today." stated Mikoto. 'Hes my new student too, but you don't need to know that.'

"I wanna be just like him! Can I meet him? Can I can I can I?" badgered the young Sasuke.

"I don't know... Hes a genin now, and he's very busy." stated Mikoto "But I suppose I could try to get him over here, Itachi kun could invite him for dinner."

* * *

-Next day-

"Settle-cough-down!" shouted Gekko as he stood at the front of the class, though only a few people stopped. "Naruto."

"Got it." stated the young blonde as he started leaking his aura, which made everyone feel like they were pinned down by a powerful thunderstorm hurricane. The class shut up and began gasping for air, as he turned up the pressure. Then, he withdrew the aura, releasing the pressure he had put on his classmates.

* * *

-Flashback, year and a half ago-

A two year old Naruto sat Cross legged in the middle of a clearing, in front of him sat Dragon and Pheonix, both cross legged as well.

"Ok Brat. We pushed you pretty hard yesterday, and Hatake started your ninjutsu training this morning, so today you learn about killing intent and aura." stated Pheonix, his right arm across his legs and his left arm in a half ram seal.

"What's aura?" questioned the small blonde.

"Aura is the refined form of killing intent. It's easier to control, but it isn't as potent... Usually..." stated Dragon.

"Usually? Does that mean that it can be?" asked Naruto.

"Yes. True masters of Aura can project massive auras that make even jonin level killer intent seem like academy students." stated Pheonix.

"Tobirama Senju and Izuna Uchiha were both masters of Aura, while Madara Uchiha and Hashirama Senju were both masters of killing intent. The current best user of aura is danzo, who is said to literally darken the area around him. The reason that Auras are lesser known then killer intent, is because that no two auras are the same, and therefore, a great aura user can't really pass on there technique, where as killing intent users use many common elements, making it easier to teach and overall easier to learn."

"What do you mean 'No two auras are alike'? Like you make up your own?" questioned the two year old.

'Minato-Sama, Kushina-Sensei... Your son is so smart, I just wish he could have the childhood you wanted for him...' thought Dragon as he observed the small blonde ball of sunshine. 'Dont you worry, we will train him and raise him until Jiraiya sama can come and take him away from all of this.'

"Not exactly Naruto. You see, Izuna Uchiha's was said to feel like you were standing in the middle of hell, like you were melting, while Tobirama's was said to feel like you were being crushed by a Tsunami." stated Pheonix.

"So it goes by your chakra nature?" asked naruto, knowing well the legacy of Tobirama Senju, also known as the second Hokage, And Izuna Uchiha, brother of Madara and rival of Tobirama.

"It can, both Tobirama and Izuna were masters of their respective elements, though it can manifest as anything, regardless of element, it goes by who you are. They were both very dangerous and outstandingly strong individuals, which is why they had such strong auras." stated Dragon. "Here, I'll demonstrate."

* * *

-Flashback end-

"Thank you." stated Gekko as he regained his breath. No matter how many times he felt the blondes aura, he had never gotten used to its intense pressure. 'I gotta improve mine. It works wonder on shutting people up. Plus I can add it to my sword style.'

'How does he do that? It's not killing intent like I've felt from father...' thought Itachi as he gazed at the near infant sitting next to him. 'He's three years old, less than half my age... And yet, he's outstandingly mature... Sometimes... Where does his strength come from?'

"...And lastly, Team Seven. Itachi Uchiha, Hana Inuzuka and Naruto. Your jonin senseis will be here shortly." stated Hayate as he walked out of the classroom.

* * *

-Timeskip, one hour-

'Well, we're the only group left.' thought Naruto. 'Guess that means that Uncle Kakashi is our sensei. I bet that the Uchiha clan won't like that. They already hate uncle Kakashi for having that eye...'

Just then, the door slid open, revealing a very attractive black haired woman in the standard kunoichi uniform, though her jonin vest was blood red. "Hello everyone, sorry I'm late, but I got tied up talking with an old friend."

"Mother?" questioned Itachi, his voice cracking slightly, getting a silent chuckle from Naruto and a giggle from Hana.

"Yes Itachi, I am your mother." stated Mikoto Dramatically in a deeper voice, gaining another silent laugh from Naruto and full blown laughter from Hana.

"Mom, you're a acting like aunt Kushina again..." stated Itachi in a chiding tone.

Naruto froze, as did Mikoto.

'Shit, does he know about who is mother was? Kakashi said he knows who his father was, but does he know about Kushina?' thought Mikoto as she watched the blondes reaction.

'Mom? So he does know who my mom is... Was...' thought Naruto, saddening himself as he remembered the picture of his mother that dragon had shown him.

"Well, as you all already know, I am Itachi's mom. But, from here on out, I am your sensei. My Name is Mikoto Uchiha." stated the Uchiha matriarch. "Now, let's begin introductions. Itachi, you go first."

"Shouldn't you go first? We all know each other, but only I know you." stated Itachi.

"Alright then." stated Mikoto, a slight glare at her son. "As I just said, my name is Mikoto Uchiha, my likes are my family, my village and my late friends. My dislikes are rapist, thugs, traitors and when my children don't listen. My goal for the future is to make you all jonin. I would like to learn my third element. And my dream... Well, for everyone in Konoha to get along again. Your turn Itachi."

'Late friend? Is she talking about mom?' thought naruto

"My name is Itachi Uchiha. I like my village, my family and peace. I dislike pointless violence, war and fan girls. My goal is to become ANBU and protect my village from the shadows. I would like to become a master of genjutsu. My Dream..." Itachi paused at this. What was his dream? He had many goals, but a dream? What did he want most? "... My dream is to make sure there is no more war."

'No more war huh? I like it.' thought naruto

'So Itachi's a passifast... Never saw that coming.' Thought Hana.

"I'll go next. My name is Hana Inuzuka. I like my dogs, my family, my village and little Naruto-chan." Stated Hana as she pinched Naruto's cheek. Naruto slapped her hand away and she huffed, annoyed that she couldn't pinch the chibis cheek. "My dislikes are rapist, traitors, Fan-boys, foul smells and cats. My goal is to become head of the inuzuka clan and find a worthy mate. I would like to mix ninjutsu and taijutsu into an improved clan fighting style. My dream is... I don't think I have one."

"That's ok Hana, dreams change, so you'll find one eventually. And it's called Nintaijutsu, the third and fourth Raikage both used it, as well as Itachis friend Shisui." smiled Mikoto. "That means your up Naruto."

"I'm Naruto. I like ramen, uncle Kakashi, training, playing shogi and toads. I dislike traitors, fangirls, snakes and girls who continuously pinch my cheeks!" stated Naruto with a glare at Hana, who smiled back. "My goal is to someday become hokage and to become the new member of the sannin, as Orochimaru no longer holds his title. I wish create a space time jutsu that surpasses the hiraishin. My dream... I want to meet a few people and find out what happened to a few..."

There were various reactions to Narutos introduction. Hana stared at him, not saying a word, though she was thinking. 'His goal is to become a sannin and hokage, and his dream is to meet a few people and find a few more? That's kinda backwards...'

Itachi had other thoughts. 'Kakashi? As in sharingan Kakashi? Is that who is raising him? It makes sense, seeing as he is Narutos fathers student... But to surpass the Flying thunder god?'

'Poor naruto... Growing up with your parents and then losing the two that raised you... You've had to grow up so fast...' thought Mikoto. "Well, now that that's settled let's go take your team test."

"Team test?" questioned Hana

"Yes, the team test. I am required to test you to see if you will make a good team. Usually the test is to put you against each other and see if you can still work together, but that won't be a problem with this group, so instead, your all going to fight me." stated Mikoto with a predatory grin, one she had not used sense the third great war when she and Kushina had come across a group from Kumo and whipped them all out.

"Meet me at training ground 45 in twenty minutes." Stated Mikoto before she disappeared in a flame shunshin.

"Hold on." stated naruto as he grabbed both Itachi and Hana and disappeared in a swirl of leafs.

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